I have run into this problem several times with Wordpress and never really found the solution.

I do not want the top level links with a drop downs to be a link to an actual page. So to remedy this my idea was to not create a page but use a custom link with # instead of the page name e.g. http://mysite.com/#/

This works fine as long as I am not on the home page, which opens to http://mysite.com/. On the home page I now have both links highlighted as active. How can I achieve this without the second link showing active?

1) Be sure you have activated the link target in the options menu on your menu page
2) Insert a custom link with no matter what link
3) select the just created custom link. click on the dropdown link on the top right side.
4) delete the link from the URL field
5) done